viral-ngs: genomic analysis pipelines for viral sequencing¶
Contents¶
- 1. Installation
- 2. Command line tools
- 2.1. taxon_filter.py - tools for taxonomic removal or filtration of reads
- 2.2. assembly.py - de novo assembly
- 2.3. interhost.py - species and population-level genetic variation
- 2.4. intrahost.py - within-host genetic variation (iSNVs)
- 2.5. read_utils.py - utilities that manipulate bam and fastq files
- 2.6. reports.py - produce various metrics and reports
- 2.7. broad_utils.py - for data generated at the Broad Institute
- 3. Using the Snakemake pipelines